Locus 3902

Sequence ID 3L_DroMel_CAF1
Location 11,300,513 – 11,300,614
Length 101
Max. P 0.826231
window6075 window6076

overview

Window 5

Location 11,300,513 – 11,300,614
Length 101
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 85.42
Mean single sequence MFE -30.57
Consensus MFE -20.46
Energy contribution -21.96
Covariance contribution 1.50
Combinations/Pair 1.10
Mean z-score -2.05
Structure conservation index 0.67
SVM decision value 0.55
SVM RNA-class probability 0.778885
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11300513 101 + 23771897
UUGGCUUCCAAAAAGGGAAGGG-----GGGGUUCCUAAGAACGAGGCCUAAGGUUCGAAUGGAUUGGAGGAUUUCCAAAGAAUUUCCCGGAAGAAAAGCUUAGAUU-
((..(((((.....((((((.(-----(..((((((((...((((.(....).))))......)))).))))..))......)))))))))))..)).........- ( -26.30)
>DroSec_CAF1 24636 102 + 1
UUGGCUUCCAAAAAGGGAAGGG-----GGGUUUCCUAAGAACGAGGCCUAAGGUCCGAAUGGGUUGGAGGAUUUCCAACGAAUUUCCCGGAAGAAAAGCUAAGAUUC
(((((((((......))))(((-----..((((........((.((((...)))))).....(((((((...)))))))))))..))).........)))))..... ( -30.50)
>DroSim_CAF1 28889 100 + 1
UUGGCUACCAAAAAGGGAAGGG-----GGGU-UCCUAAGAACGAGGCCUAAGGUCCGAAUGGGUUGGAGGAUUUCCAACGAAUUUCCCGGAAGAAAAGCAAAGAUU-
...(((.((.....))...(((-----..((-((.......((.((((...)))))).....(((((((...)))))))))))..)))........))).......- ( -29.40)
>DroEre_CAF1 28214 99 + 1
UUGGGUUCCUA-------AAGGGGAUGGGGGUUCCUAAGAACGAGGCCGAAGGUCCGGAUGGGUUGGAGGAUUUCCAACCCAUUUCCCGGAAGAAAACCUAAGAUC-
((((((((((.-------...))))(((((((((....))))..((.(....).)).((((((((((((...))))))))))))))))).......))))))....- ( -36.10)
>consensus
UUGGCUUCCAAAAAGGGAAGGG_____GGGGUUCCUAAGAACGAGGCCUAAGGUCCGAAUGGGUUGGAGGAUUUCCAACGAAUUUCCCGGAAGAAAAGCUAAGAUU_
(((((((.......((((((.......((((.((((..((.((.((((...))))))......))..)))).))))......)))))).......)))))))..... (-20.46 = -21.96 +   1.50)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 11,300,513 – 11,300,614
Length 101
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 85.42
Mean single sequence MFE -24.10
Consensus MFE -16.49
Energy contribution -16.93
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -2.10
Structure conservation index 0.68
SVM decision value 0.70
SVM RNA-class probability 0.826231
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11300513 101 - 23771897
-AAUCUAAGCUUUUCUUCCGGGAAAUUCUUUGGAAAUCCUCCAAUCCAUUCGAACCUUAGGCCUCGUUCUUAGGAACCCC-----CCCUUCCCUUUUUGGAAGCCAA
-.......((((((.....(((((.....(((((.....)))))...............((....((((....))))...-----.))))))).....))))))... ( -19.70)
>DroSec_CAF1 24636 102 - 1
GAAUCUUAGCUUUUCUUCCGGGAAAUUCGUUGGAAAUCCUCCAACCCAUUCGGACCUUAGGCCUCGUUCUUAGGAAACCC-----CCCUUCCCUUUUUGGAAGCCAA
((((....((((....((((((......((((((.....))))))...))))))....))))...))))...(....)..-----..(((((......))))).... ( -22.50)
>DroSim_CAF1 28889 100 - 1
-AAUCUUUGCUUUUCUUCCGGGAAAUUCGUUGGAAAUCCUCCAACCCAUUCGGACCUUAGGCCUCGUUCUUAGGA-ACCC-----CCCUUCCCUUUUUGGUAGCCAA
-.......(((........(((((....((((((.....))))))......((..((((((.......)))))).-.)).-----...)))))........)))... ( -20.39)
>DroEre_CAF1 28214 99 - 1
-GAUCUUAGGUUUUCUUCCGGGAAAUGGGUUGGAAAUCCUCCAACCCAUCCGGACCUUCGGCCUCGUUCUUAGGAACCCCCAUCCCCUU-------UAGGAACCCAA
-......(((((....(((((...((((((((((.....))))))))))))))).....))))).((((((((((.......)))....-------))))))).... ( -33.80)
>consensus
_AAUCUUAGCUUUUCUUCCGGGAAAUUCGUUGGAAAUCCUCCAACCCAUUCGGACCUUAGGCCUCGUUCUUAGGAAACCC_____CCCUUCCCUUUUUGGAAGCCAA
........((((((..((((((......((((((.....))))))...))))))(((.(((......))).)))........................))))))... (-16.49 = -16.93 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:35 2006